Research workbench
Transaldolase from bacillus subtilis
Analyse Transaldolase from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R8R
- Type
- protein
- Length
- 4,196 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaldolase
- EC
- 2.2.1.2
- UniProt
- P19669
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 9 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, V, M, W, R, T, U | Transaldolase (EC 2.2.1.2) | protein | 212 | 52% helix, 19% strand | P19669 |
| C | Transaldolase (EC 2.2.1.2) | protein | 204 | 50% helix, 21% strand | P19669 |
| D | Transaldolase (EC 2.2.1.2) | protein | 207 | 53% helix, 19% strand | P19669 |
| H | Transaldolase (EC 2.2.1.2) | protein | 211 | 52% helix, 19% strand | P19669 |
| I | Transaldolase (EC 2.2.1.2) | protein | 210 | 54% helix, 20% strand | P19669 |
| J | Transaldolase (EC 2.2.1.2) | protein | 206 | 52% helix, 20% strand | P19669 |
| K, L | Transaldolase (EC 2.2.1.2) | protein | 211 | 52% helix, 19% strand | P19669 |
| N | Transaldolase (EC 2.2.1.2) | protein | 202 | 51% helix, 20% strand | P19669 |
| P | Transaldolase (EC 2.2.1.2) | protein | 202 | 51% helix, 20% strand | P19669 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C, D, E, F, G, H, I, J, V, K, L, M, N, W, P, R, T, U
- GOL · Glycerol · additive · 10 copies · chains A, B, E, F, G, H, V, L, W, R, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.65 | 0.84 | 30 | empty |
| 2 | 201 | 0.65 | 0.84 | 29 | empty |
| 3 | 207 | 0.63 | 0.83 | 31 | empty |
| 4 | 215 | 0.63 | 0.83 | 36 | empty |
| 5 | 201 | 0.63 | 0.83 | 31 | empty |
Interfaces
51 interfaces between chains.
- W–P · 1580 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1569 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 1563 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1558 Ų buried · 17 hydrogen bonds · protein-protein
- R–T · 1558 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3R8R · Transaldolase from Bacillus subtilis · the same entry in another collection · chain V against V, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P19669
- Elsewhere: RCSB PDB 3R8R · PDBe 3R8R · UniProt P19669
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